Studies on the pathogenesis of autoimmune diseases have begun to delve into the molecular and cellular mechanisms, and transcription factors, as key regulators of immune effector cell development and function, have received growing attention. Their involvement has been investigated in immune cells, such as T and B lymphocytes, macrophages and neutrophils, but also end-organ tissues, such as synoviocytes, keratinocytes and epithelial cells, and has revealed particularly dominant roles for NF-kappaB, STAT and AP-1 family members. This review summarizes recent findings and current knowledge regarding the roles of transcription factors in autoimmunity, focusing on their role in pathogenesis, as evidenced by both biological and genetic studies, as well as the implications of these findings for anti-inflammatory therapies.